Are these 2 security keys taking the place of the 2-Step keys used to validate 3rd party apps?

I suspect you are describing two separate subjects.

Security keys for Apple ID are devices intended to prevent unauthorized use of your Apple ID. About Security Keys for Apple ID - Apple Support describes how to use them.

Validating third party apps is another subject altogether. An answer depends on whether you are developing software for use on Apple products, or if you merely intend to install and use apps developed by others.

Please read the following user tip and restate your question/problem in detail: 

     Writing an Effective Apple Support Communities Question - Apple Community

What 2 security keys?

When do you encounter them?

What apps?

What system version are you running?